I thought the plan was to not domesticate the same animals, to help make this a bit different from the actual world.

This is why I added a couple of alternatives. Cormorant, capybara, ratites, even iguanas. Not to mention the three alternative carnivores skunk, polecat and mongoose.

Also, the distributions also sometimes lead to interesting results. Just consider that horses are only available in the new world and the old world only has elephants and dromedaries in terms of mounts.

In the end, you don't need to change everything in order to create something new. Replacing only cats/dogs with something else or horses with camels would already lead to a sufficiently different feel, even if there are goats, sheep and oxen.

One thing I want to mention though is that some animals are harder to domesticate and yet some harder-to-domesticate animals have been domesticated in the real world while others have not, or at least not as much. Maybe some sort of "luck" factor should be involved when attempting domestication. For example, horses have been domesticated in asia. In north america, however, the remaining horses were hunted to extinction. Similarly, emus were never domesticated in australia while the aurochs was in europe, despite the aurochs being meaner and harder to tame than emus.

Edit:One thing to consider: The invention of the (cart) wheel has been attributed to the presence of draft animals. The americas, for instance, which lacked domesticated bovines and equines never got to invent the wheel, because humans move weight more efficiently by carrying it, rather than pulling it. And llamas were used primarily by mountain societies, which hindered the usage of wheels. Same for the dromedary, which was mostly used in sandy areas. Carrying stuff on the animal's back was easier.

Just to be clear, those awesome maps Flisch made are the state of animals at the END of the phase (Phase II) we are about to enter. Lot's of weird stuff happens between 200,000ya and when those maps become relevant. Just look at the modern distribution of animals like the Camelids or the tapirs. So, I wouldn't worry too much about how things will get where they will.

And yes, at the start of Phase III, anything that was alive during the Holocene or later should stay alive unless we kill them again. This article should be of some help in that regard: https://en.wikipedia.org/wiki/Holocene_extinction. At the very end of that article in the "See Also"section, there are some links to "recently extinct" lists that can also be helpful.

Edit: I will add though that species that went extinct due to reasons other than humans should still go extinct at their regular times (sorry Woolly Mammoth fans!).

Okay but I'm still gonna domesticate otters and turtles. And are we still doing near-prehistoric creatures? I want moas.

I don't know how realistic you want to have this, but I tried to stick to animals that have a realistic chance of being domesticated.

I mean, if you want, you can give me a list with animals you want to have added. I was thinking of adding the bison for example. I don't think it's much harder to domesticate than the aurochs. I just wasn't even sure if you people would be using this, so I restricted myself to the more likely candidates.

Starting island is roughly Indonesia, yeah? I was looking at the stuff native to Indonesia. There are turtles and otters, so I'm good. As for how realistic we want to have this, that's a very good and running question for the game.

How would we be using the animal habitat map? I thought it was examples of where certain species would be.